16-11050352-C-G

Variant names:

• chr16-11050352-C-G
• rs9302458
• NM_015226.3:c.1867-1161C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015226.3(CLEC16A):​c.1867-1161C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,154 control chromosomes in the GnomAD database, including 5,627 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.23 (5627 hom., cov: 33)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494
• Publications: 7 publications found

Genes affected

CLEC16A (HGNC:29013): (C-type lectin domain containing 16A) This gene encodes a member of the C-type lectin domain containing family. Single nucleotide polymorphisms in introns of this gene have been associated with diabetes mellitus, multiple sclerosis and rheumatoid arthritis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

CLEC16A Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015226.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	NM_015226.3	MANE Select	c.1867-1161C>G		intron	N/A	NP_056041.1	Q2KHT3-1
	CLEC16A	NM_001410905.1		c.1861-1161C>G		intron	N/A	NP_001397834.1	A0A8V8TR67
	CLEC16A	NM_001243403.2		c.1813-1161C>G		intron	N/A	NP_001230332.1	Q2KHT3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	ENST00000409790.6	TSL:5 MANE Select	c.1867-1161C>G		intron	N/A	ENSP00000387122.1	Q2KHT3-1
	CLEC16A	ENST00000409552.4	TSL:1	c.1813-1161C>G		intron	N/A	ENSP00000386495.3	Q2KHT3-2
	CLEC16A	ENST00000904405.1		c.1861-1161C>G		intron	N/A	ENSP00000574464.1

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34335 AN: 152036 Hom.: 5601 Cov.: 33

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.198

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.226 AC: 34417 AN: 152154 Hom.: 5627 Cov.: 33 AF XY: 0.222 AC XY: 16533 AN XY: 74380

African (AFR) AF: 0.465 AC: 19284 AN: 41464

American (AMR) AF: 0.146 AC: 2230 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 544 AN: 3470

East Asian (EAS) AF: 0.119 AC: 616 AN: 5180

South Asian (SAS) AF: 0.148 AC: 713 AN: 4822

European-Finnish (FIN) AF: 0.153 AC: 1623 AN: 10596

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8836 AN: 68020

Other (OTH) AF: 0.200 AC: 420 AN: 2102

Alfa AF: 0.0902 Hom.: 148

Bravo AF: 0.237

Asia WGS AF: 0.163 AC: 564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.41
DANN	Benign	0.42
PhyloP100		-0.49
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9302458; hg19: chr16-11144209;